Contacts of the helix formed by residues 168 - 177 (chain A) in PDB entry 5XRZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.4 24.1 + - - +
165A CYS* 2.9 21.6 + - + +
166A ILE 3.4 0.2 - - - -
167A LEU* 1.3 75.3 - - - +
169A LYS* 1.3 69.4 + - - +
170A ASP* 3.7 9.6 + - - +
171A TYR* 3.1 21.5 + - + +
172A LEU* 3.0 23.5 + - - +
69K HIS* 3.7 24.8 + - + +
70K ARG* 4.1 14.0 + - - -
186K VAL* 4.4 5.2 - - - +
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Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU 3.4 7.4 + - - +
168A ASP* 1.3 74.2 + - - +
170A ASP* 1.3 61.2 + - - +
172A LEU* 3.1 15.0 + - + +
173A ARG* 2.9 34.8 + - + +
53K SER* 6.2 0.2 - - - -
65K TYR* 4.3 12.3 + - - -
67K GLU* 3.6 37.3 + - - +
69K HIS* 5.1 0.8 + - - -
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.3 7.5 + - - +
169A LYS* 1.3 78.5 - - - +
171A TYR* 1.3 59.4 + - - +
173A ARG* 3.2 27.8 + - - +
174A SER* 2.9 31.4 + - - -
70K ARG* 4.2 16.5 + - - -
183K PRO* 3.8 11.4 - - - +
184K LEU* 3.8 31.5 + - - +
186K VAL* 3.6 18.8 - - + -
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.5 31.0 - - + +
47A LEU* 2.3 45.7 + - - +
52A ILE* 3.9 8.7 - - + +
165A CYS* 3.1 39.5 - - + -
166A ILE* 4.5 4.9 - - + -
168A ASP* 3.1 26.0 + - + +
170A ASP* 1.3 78.3 - - - +
172A LEU* 1.3 62.5 + - + +
174A SER* 3.3 2.6 + - - -
175A LEU* 2.9 55.3 + - + +
186K VAL* 3.7 10.3 - - - +
188K LEU* 3.6 21.8 - - + -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 6.6 0.2 - - + -
64A CYS* 3.7 39.7 - - + +
166A ILE* 4.0 23.8 - - + +
167A LEU 5.8 0.9 - - - -
168A ASP 3.0 16.0 + - - +
169A LYS* 3.5 15.0 - - + +
171A TYR* 1.3 79.3 - - + +
173A ARG* 1.3 64.9 + - + +
175A LEU* 2.9 31.2 + - + +
176A ASN* 3.0 23.4 + - - +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LYS* 2.9 18.7 + - + +
170A ASP* 3.2 33.7 + - - +
172A LEU* 1.3 76.2 - - + +
174A SER* 1.3 63.0 + - - +
176A ASN* 3.4 19.0 + - - +
177A LYS* 3.3 48.9 + - - +
183K PRO* 3.6 19.5 + - - +
184K LEU 3.5 18.6 + - - -
185K GLU* 5.1 3.0 - - - +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASP 2.9 17.2 + - - -
171A TYR 3.7 4.7 - - - -
173A ARG* 1.3 75.2 + - - +
175A LEU* 1.3 64.3 + - - +
177A LYS* 3.3 30.8 + - - +
178A LEU* 3.9 3.1 - - - +
185K GLU* 4.8 4.0 - - - +
186K VAL* 3.0 41.0 + - - +
188K LEU* 3.3 21.9 - - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU 4.5 1.3 - - - +
49A PRO* 4.1 34.0 - - + +
52A ILE* 3.8 25.8 - - + -
64A CYS* 5.5 2.9 - - - -
171A TYR* 2.9 51.5 + - + +
172A LEU* 2.9 25.7 + - + +
174A SER* 1.3 75.6 - - - +
176A ASN* 1.3 66.1 + - - +
177A LYS 3.1 1.0 + - - -
178A LEU* 3.4 17.8 + - + +
188K LEU* 3.9 13.7 - - + -
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Residues in contact with ASN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LYS* 5.1 12.0 + - - +
64A CYS* 5.6 6.2 - - - -
172A LEU* 3.0 28.5 + - - +
173A ARG* 3.7 13.3 - - - +
174A SER 3.4 0.2 - - - -
175A LEU* 1.3 76.0 - - - +
177A LYS* 1.3 58.1 + - + +
178A LEU 3.2 10.2 + - - +
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.3 47.0 - - - +
174A SER* 3.3 17.2 + - - +
175A LEU 3.1 1.8 - - - -
176A ASN* 1.3 77.4 - - + +
178A LEU* 1.3 66.6 + - - +
179A PRO* 4.6 1.4 - - - +
185K GLU* 5.1 13.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il